tbuckley/cabot-search huggingface dataset:
Error-corrected next-generation sequencing to advance nonclinical genotoxicity and carcinogenicity testing
Authors: Francesco Marchetti, Renato Cardoso, Connie L. Chen, George R. Douglas, Joanne Elloway, Patricia A. Escobar, Tod Harper Jr, Robert H. Heflich, Darren Kidd, Anthony M. Lynch, Meagan B. Myers, Barbara L. Parsons, Jesse J. Salk, Raja S. Settivari, Stephanie L. Smith-Roe, Kristine L. Witt, Carole Yauk, Robert R. Young, Shaofei Zhang, Sheroy Minocherhomji
Journal: Nature Reviews Drug Discovery (2023)
PRISMA AI reporting guidelines for systematic reviews and meta-analyses on AI in healthcare
Authors: Giovanni E. Cacciamani, Timothy N. Chu, Daniel I. Sanford, Andre Abreu, Vinay Duddalwar, Assad Oberai, C.-C. Jay Kuo, Xiaoxuan Liu, Alastair K. Denniston, Baptiste Vasey, Peter McCulloch, Robert F. Wolff, Sue Mallett, John Mongan, Charles E. Kahn, Viknesh Sounderajah, Ara Darzi, Philipp Dahm, Karel G. M. Moons, Eric Topol, Gary S. Collins, David Moher, Inderbir S. Gill, Andrew J. Hung
Journal: Nature Medicine (2023)
Of Pandemics and Renewals
Authors: Diane M. Birnbaumer
Journal: Annals of Internal Medicine (2023)

On Being a DoctorJanuary 2023Of Pandemics and RenewalsDiane M. Birnbaumer, MDDiane M. Birnbaumer, MDHarbor–UCLA Medical Center, Torrance, CaliforniaSearch for more papers by this authorAuthor, Article, and Disclosure Informationhttps://doi.org/10.7326/M22-2847 Audio Reading - “Of Pandemics and Renewals” Audio. Virginia L. Hood, MD, a physician from the University of Vermont, reads “Of Pandemics and Renewals” by Diane M. Birnbaumer, MD Your browser does not support the audio element. Audio player progress bar Step backward in current audio track Play current audio trackPause current audio track Step forward in current audio track Mute current audio trackUnmute current audio track 00:00/ SectionsAboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinkedInRedditEmail ONEI am a newly minted doctor, and I'm terrified.The year is 1984; the city is San Francisco; and the place is Ward 5B, the first hospital ward dedicated solely to the care of patients suffering from AIDS.My job is to take care of these men during the long nights I'm on call.Do I know enough? Will I hurt someone? Can I actually do this?I spent the past 4 years learning the Latin-laced lingo of medicine. My brain is a maelstrom of facts and data. Yet, I cannot even seem to manage the task of clipping ... Author, Article, and Disclosure InformationAffiliations: Harbor–UCLA Medical Center, Torrance, CaliforniaCorresponding Author: Diane M. Birnbaumer, MD, Department of Emergency Medicine, Harbor–UCLA Medical Center, Box 21, Torrance, CA 90509; e-mail, [email protected]com. PreviousarticleNextarticle Advertisement Audio Reading - “Of Pandemics and Renewals” Audio. Virginia L. Hood, MD, a physician from the University of Vermont, reads “Of Pandemics and Renewals” by Diane M. Birnbaumer, MD Your browser does not support the audio element. Audio player progress bar Step backward in current audio track Play current audio trackPause current audio track Step forward in current audio track Mute current audio trackUnmute current audio track 00:00/ FiguresReferencesRelatedDetails Metrics January 2023Volume 176, Issue 1Page: 139 ePublished: 17 January 2023 Issue Published: January 2023 Copyright & PermissionsCopyright © 2023 by American College of Physicians. All Rights Reserved.PDF downloadLoading ...
Annals Consult Guys - Care of a Patient With Left Ventricular Thrombus
Authors: Howard H. Weitz, Geno J. Merli
Journal: Annals of Internal Medicine (2023)

Web ExclusivesJanuary 2023Annals Consult Guys - Care of a Patient With Left Ventricular ThrombusFREEHoward H. Weitz, MD and Geno J. Merli, MDHoward H. Weitz, MDThomas Jefferson University, Philadelphia, Pennsylvania (H.H.W., G.J.M.)Search for more papers by this author and Geno J. Merli, MDThomas Jefferson University, Philadelphia, Pennsylvania (H.H.W., G.J.M.)Search for more papers by this authorAuthor, Article, and Disclosure Informationhttps://doi.org/10.7326/W22-0014 CME/MOC SectionsSupplemental MaterialAboutVisual Abstract ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinkedInRedditEmail The Annals Consult Guys discuss the management of patients with left ventricular thrombus. Who is at risk? How should left ventricular thrombus be treated and monitored?For more videos from and information on Annals Consult Guys, visit go.annals.org/ConsultGuys. Comments0 CommentsSign In to Submit A Comment Author, Article, and Disclosure InformationAuthors: Howard H. Weitz, MD; Geno J. Merli, MDAffiliations: Thomas Jefferson University, Philadelphia, Pennsylvania (H.H.W., G.J.M.)Disclosures: Drs. Merli and Weitz report that they have no financial relationships or interests to disclose. All relevant financial relationships have been mitigated. Forms can be viewed at www.acponline.org/authors/icmje/ConflictOfInterestForms.do?msNum=W22-0014.Editors' Disclosures: The editors have no relevant financial relationships to disclose. Individual forms may be viewed at www.annals.org/editorsdisclosures. PreviousarticleNextarticle Advertisement FiguresReferencesRelatedDetails Metrics January 2023Volume 176, Issue 1 ePublished: 17 January 2023 Issue Published: January 2023 Copyright & PermissionsCopyright © 2023 by American College of Physicians. All Rights Reserved.Loading ...
Hydroxychloroquine Dose and Risk for Incident Retinopathy
Authors: Ronald B. Melles, April M. Jorge, Michael F. Marmor, Baijun Zhou, Carol Conell, Jingbo Niu, Natalie McCormick, Yuqing Zhang, Hyon K. Choi
Journal: Annals of Internal Medicine (2023)

Hydroxychloroquine is recommended for all patients with systemic lupus erythematosus and is often used for other inflammatory conditions, but a critical long-term adverse effect is vision-threatening retinopathy.To characterize the long-term risk for incident hydroxychloroquine retinopathy and examine the degree to which average hydroxychloroquine dose within the first 5 years of treatment predicts this risk.Cohort study.U.S. integrated health network.All patients aged 18 years or older who received hydroxychloroquine for 5 or more years between 2004 and 2020 and had guideline-recommended serial retinopathy screening.Hydroxychloroquine dose was assessed from pharmacy dispensing records. Incident hydroxychloroquine retinopathy was assessed by central adjudication of spectral domain optical coherence tomography with severity assessment (mild, moderate, or severe). Risk for hydroxychloroquine retinopathy was estimated over 15 years of use according to hydroxychloroquine weight-based dose (>6, 5 to 6, or ≤5 mg/kg per day) using the Kaplan-Meier estimator.Among 3325 patients in the primary study population, 81 developed hydroxychloroquine retinopathy (56 mild, 17 moderate, and 8 severe), with overall cumulative incidences of 2.5% and 8.6% at 10 and 15 years, respectively. The cumulative incidences of retinopathy at 15 years were 21.6% for higher than 6 mg/kg per day, 11.4% for 5 to 6 mg/kg per day, and 2.7% for 5 mg/kg per day or lower. The corresponding risks for moderate to severe retinopathy at 15 years were 5.9%, 2.4%, and 1.1%, respectively.Possible misclassifications of dose due to nonadherence to filled prescriptions.In this large, contemporary cohort with active surveillance retinopathy screening, the overall risk for hydroxychloroquine retinopathy was 8.6% after 15 years, and most cases were mild. Higher hydroxychloroquine dose was associated with progressively greater risk for incident retinopathy.National Institutes of Health.
Epstein–Barr Viral Load Monitoring Strategy and the Risk for Posttransplant Lymphoproliferative Disease in Adult Liver Transplantation
Authors: Bastian N. Ruijter, Ron Wolterbeek, Mitchell Hew, Marjolein van Reeven, Danny van der Helm, Jeroen Dubbeld, Maarten E. Tushuizen, Herold Metselaar, Ann C.T.M. Vossen, Bart van Hoek
Journal: Annals of Internal Medicine (2023)

Background: Primary infection with or reactivation of Epstein–Barr virus (EBV) can occur after liver transplant (LT) and can lead to posttransplant lymphoproliferative disease (PTLD). In pediatric LT, an EBV-DNA viral load (EBV VL) monitoring strategy, including the reduction of immunosuppression, has led to a lower incidence of PTLD. For adult LT recipients with less primary infection and more EBV reactivation, it is unknown whether this strategy is effective. Objective: To examine the effect of an EBV VL monitoring strategy on the incidence of PTLD after LT in adults. Design: Cohort study. Setting: Two university medical centers in the Netherlands. Patients: Adult recipients of first LT in Leiden between September 2003 and January 2017 with an EBV VL monitoring strategy formed the monitoring group (M1), recipients of first LT in Rotterdam between January 2003 and January 2017 without such a strategy formed the contemporary control group (C1), and those who had transplants in Leiden between September 1992 and September 2003 or Rotterdam between 1986 and January 2003 formed the historical control groups (M0 and C0, respectively). Measurements: Influence of EBV VL monitoring on incidence of PTLD. Results: After inverse probability of treatment weighting of the 4 groups to achieve a balance among the groups for important patient characteristics, differences within hospitals between the historical and recent era in cumulative incidences—expressed as the number of events per 1000 patients measured at 5-, 10-, and 15-year follow-up—showed fewer events in the contemporary era in both centers. This difference was considerably larger in the monitoring center, whereas the 95% CI included the null value of 0 for point estimates. Limitation: Retrospective, low statistical power, and incompletely balanced groups, and non-EBV PTLD cannot be prevented. Conclusion: Monitoring EBV VL may reduce PTLD incidence after LT in adults; larger studies are warranted. Primary Funding Source: None.
Long-Term Regression after Discontinuation of Regorafenib Administered for Sorafenib-Refractory Hepatocellular Carcinoma
Authors: Heewon Bae, Je Ryung Gil, Moon Hyung Lee, Taekyu Lim
Journal: Liver Cancer (2023)

A patient with hepatocellular carcinoma(HCC) staged Barcelona Clinic for Liver Cancer stage B started chemotherapy because of intrahepatic recurrence after hepatic segmentectomy. Regorafenib was started as a second-line treatment due to refractory to sorafenib treatment, but was discontinued after 26 months due to side effects. After two years of follow-up, the patients achieved unexpected long-term regression. We present the potential of regorafenib effect for anti-tumor immunity through possible pharmacological mechanisms.
Annals On Call - Endemic Mycoses
Authors: Robert M. Centor, George R. Thompson III
Journal: Annals of Internal Medicine (2023)

Web ExclusivesJanuary 2023Annals On Call - Endemic MycosesFREERobert M. Centor, MD and George R. Thompson III, MDRobert M. Centor, MDHuntsville Regional Medical Campus, University of Alabama Birmingham School of Medicine, Birmingham, Alabama (R.M.C.)Search for more papers by this author and George R. Thompson III, MDDepartment of Internal Medicine, Division of Infectious Diseases, and Department of Medical Microbiology and Immunology, University of California-Davis Medical Center, Sacramento, California (G.R.I.)Search for more papers by this authorAuthor, Article, and Disclosure Informationhttps://doi.org/10.7326/A22-0002 CME/MOC SectionsAboutVisual Abstract ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinkedInRedditEmail In this episode of Annals On Call, Dr. Centor discusses endemic mycoses with Dr. George Thompson.Annals articles discussed include...Endemic Mycoses: Underdiagnosed and Underreported: https://www.acpjournals.org/doi/full/10.7326/M22-2371About Annals On CallAnnals On Call focuses on a clinically influential article published in Annals of Internal Medicine. Dr. Robert Centor shares his own perspective on the material and interviews topic area experts to discuss, debate, and share diverse insights about patient care and health care delivery.For more information on Annals On Call and for more episodes, visit go.annals.org/OnCall. Comments0 CommentsSign In to Submit A Comment Author, Article, and Disclosure InformationAuthors: Robert M. Centor, MD; George R. Thompson III, MDAffiliations: Huntsville Regional Medical Campus, University of Alabama Birmingham School of Medicine, Birmingham, Alabama (R.M.C.)Department of Internal Medicine, Division of Infectious Diseases, and Department of Medical Microbiology and Immunology, University of California-Davis Medical Center, Sacramento, California (G.R.I.)Disclosures: All relevant financial relationships have been mitigated. Disclosures can be viewed at www.acponline.org/authors/icmje/ConflictOfInterestForms.do?msNum=A22-0002.Editors' Disclosures: The editors have no relevant financial relationships to disclose. Individual forms may be viewed at www.annals.org/editorsdisclosures. PreviousarticleNextarticle Advertisement FiguresReferencesRelatedDetailsSee AlsoEndemic Mycoses: Underdiagnosed and Underreported George R. Thompson III and Tom M. Chiller Metrics January 2023Volume 176, Issue 1 ePublished: 17 January 2023 Issue Published: January 2023 Copyright & PermissionsCopyright © 2023 by American College of Physicians. All Rights Reserved.Loading ...
Grief's Terrain
Authors: Martin M. Ellbogen
Journal: Annals of Internal Medicine (2023)

Ad LibitumJanuary 2023Grief's TerrainMartin H. Ellbogen Jr., MDMartin H. Ellbogen Jr., MDNordland, WashingtonSearch for more papers by this authorAuthor, Article, and Disclosure Informationhttps://doi.org/10.7326/M22-0316 Audio Reading - “Grief's Terrain” Audio. Michael A. Lacombe, MD, Annals Associate Editor, reads “Grief's Terrain” by Martin H. Ellbogen Jr., MD Your browser does not support the audio element. Audio player progress bar Step backward in current audio track Play current audio trackPause current audio track Step forward in current audio track Mute current audio trackUnmute current audio track 00:00/ SectionsAboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinkedInRedditEmail After she died I lapsedInto release,Clung to myths for a while,Scraped my knees chasing rabbits into holesBut felt no pain,Reached for low branchesBut had no gripAnd let go, landing but not hard enough to come to,Sought answers from the sage and the streamsBut could no longer translate their voice,Could no longer find comfort in the stars or their maker,Know intimacy in an old embraceOr see enough lightTo read the signs.And here is where it has led meShe was ... Author, Article, and Disclosure InformationAffiliations: Nordland, WashingtonCorresponding Author: Martin H. Ellbogen Jr., MD; e-mail, [email protected]com.Correction: This article was corrected on 23 January 2023 to correct the author's middle initial. PreviousarticleNextarticle Advertisement Audio Reading - “Grief's Terrain” Audio. Michael A. Lacombe, MD, Annals Associate Editor, reads “Grief's Terrain” by Martin H. Ellbogen Jr., MD Your browser does not support the audio element. Audio player progress bar Step backward in current audio track Play current audio trackPause current audio track Step forward in current audio track Mute current audio trackUnmute current audio track 00:00/ FiguresReferencesRelatedDetails Metrics January 2023Volume 176, Issue 1Page: 140 ePublished: 17 January 2023 Issue Published: January 2023 Copyright & PermissionsCopyright © 2023 by American College of Physicians. All Rights Reserved.PDF downloadLoading ...
Model to predict major complications following liver resection for HCC in patients with metabolic syndrome
Authors: Giammauro Berardi, Francesca Ratti, Carlo Sposito, Martina Nebbia, Daniel M. D’Souza, Franco Pascual, Epameinondas Dogeas, Samer Tohme, Francesco E. D’Amico, Remo Alessandris, Ilaria Simonelli, Celeste Del Basso, Nadia Russolillo, Amika Moro, Guido Fiorentini, Matteo Serenari, Fernando Rotellar, Giuseppe Zimmitti, Simone Famularo, Tommy Ivanics, Daniel Hoffman, Edwin Onkendi, Yasmin Essaji, Santiago Lopez Ben, Celia Caula, Gianluca Rompianesi, Asmita Chopra, Mohammed Abu Hilal, Guido Torzilli, Gonzalo Sapisochin, Carlos Corvera, Adnan Alseidi, Scott Helton, Roberto I. Troisi, Kerri Simo, Claudius Conrad, Matteo Cescon, Sean Cleary, Choon H.D. Kwon, Alessandro Ferrero, Giuseppe M. Ettorre, Umberto Cillo, David Geller, Daniel Cherqui, Pablo E. Serrano, Cristina Ferrone, Vincenzo Mazzaferro, Luca Aldrighetti, T. Peter Kingham
Journal: Hepatology (2023)

Background: Metabolic syndrome (MS) is rapidly growing as risk factor for HCC. Liver resection for HCC in patients with MS is associated with increased postoperative risks. There are no data on factors associated with postoperative complications. Aims: The aim was to identify risk factors and develop and validate a model for postoperative major morbidity after liver resection for HCC in patients with MS, using a large multicentric Western cohort. Materials and Methods: The univariable logistic regression analysis was applied to select predictive factors for 90 days major morbidity. The model was built on the multivariable regression and presented as a nomogram. Performance was evaluated by internal validation through the bootstrap method. The predictive discrimination was assessed through the concordance index. Results: A total of 1087 patients were gathered from 24 centers between 2001 and 2021. Four hundred and eighty-four patients (45.2%) were obese. Most liver resections were performed using an open approach (59.1%), and 743 (68.3%) underwent minor hepatectomies. Three hundred and seventy-six patients (34.6%) developed postoperative complications, with 13.8% major morbidity and 2.9% mortality rates. Seven hundred and thirteen patients had complete data and were included in the prediction model. The model identified obesity, diabetes, ischemic heart disease, portal hypertension, open approach, major hepatectomy, and changes in the nontumoral parenchyma as risk factors for major morbidity. The model demonstrated an AUC of 72.8% (95% CI: 67.2%–78.2%) (https://childb.shinyapps.io/NomogramMajorMorbidity90days/). Conclusions: Patients undergoing liver resection for HCC and MS are at high risk of postoperative major complications and death. Careful patient selection, considering baseline characteristics, liver function, and type of surgery, is key to achieving optimal outcomes.
Does oxidative stress shorten telomeres in vivo? A meta-analysis
Authors: Emma Armstrong, Jelle Boonekamp
Journal: Ageing Research Reviews (2023)

Telomere attrition is considered a hallmark of ageing. Untangling the proximate causes of telomere attrition may therefore reveal important aspects about the ageing process. In a landmark paper in 2002 Thomas von Zglinicki demonstrated that oxidative stress accelerates telomere attrition in cell culture. In the next 20 years, oxidative stress became firmly embedded into modern theories of ageing and telomere attrition. However, a recent surge of in vivo studies reveals an inconsistent pattern questioning the unequivocal role of oxidative stress in telomere length and telomere attrition (henceforth referred to as telomere dynamics), in living organisms. Here we report the results of the first formal meta-analysis on the association between oxidative stress and telomere dynamics in vivo, representing 37 studies, 4969 individuals, and 18,677 correlational measurements. The overall correlation between oxidative stress markers and telomere dynamics was indistinguishable from zero (r = 0.027). This result was independent of the type of oxidative stress marker, telomere dynamic, or taxonomic group. However, telomere measurement method affected the analysis and the subset of TRF-based studies showed a significant overall correlation (r = 0.09), supporting the prediction that oxidative stress accelerates telomere attrition. The correlation was more pronounced in short-lived species and during the adult life phase, when ageing becomes apparent. We then performed an additional meta-analysis of interventional studies (n = 7) manipulating oxidative stress. This revealed a significant effect of treatment on telomere dynamics (d=0.36). Our findings provide new support for the hypothesis that oxidative stress causes telomere attrition in living organisms.
The role of IgG1 and IgG4 as dominant IgE-blocking antibodies shifts during allergen immunotherapy
Authors: Maria R. Strobl, Hilal Demir, Gabriela Sánchez Acosta, Anja Drescher, Claudia Kitzmüller, Christian Möbs, Wolfgang Pfützner, Barbara Bohle
Journal: Journal of Allergy and Clinical Immunology (2023)
Recanalization using a novel drill-shaped dilator for a severe pancreatic duct stricture and impacted pancreatic duct stone
Authors: Hideyuki Shiomi, Ryota Nakano, Shogo Ota, Takashi Nishimura, Hirayuki Enomoto, Hiroko Iijima
Journal: Endoscopy (2023)

Pancreatic duct stones can cause severe acute pancreatitis and are sometimes fatal. Endoscopic pancreatic duct drainage has been established as a first-line treatment [1] [2]; however, hard stones can make passing through strictures challenging. A Soehendra stent retriever with a screw tip (SSR-7; Cook Medical, Tokyo, Japan) may be useful in this situation [3], but a serious complication can occur should the tip of the stent retriever detach and migrate into the pancreatic duct [4]. A novel dilator with a unique shape was recently developed (Tornus ES for 0.025-inch guidewire; 7 Fr, stainless steel; Asahi Intecc, Aichi, Japan) [5] ([Fig. 1]). This drill-shaped dilator can be rotated to break through strictures. Here, we describe recanalization using this novel drill-shaped dilator for a patient with severe pancreatic duct stricture and an impacted pancreatic duct stone ([Video 1]).
Water-immersion and cap-assisted endoscopic ablation of hemorrhagic radiation proctopathy with a novel 1.9/1.5-μm dual-emission endoscopic laser treatment
Authors: Gian Eugenio Tontini, Alessandro Rimondi, Flaminia Cavallaro, Nicoletta Nandi, Lucia Scaramella, Maurizio Vecchi, Luca Elli
Journal: Endoscopy (2023)

Hemorrhagic radiation proctopathy is a long-lasting side effect of radiotherapy for gynecologic, urologic, and digestive cancers that is characterized by hematochezia from mucosal angioectasia, and a variable degree of rectal pain, tenesmus, urgency, and incontinence [1]. When symptoms or anemia occur despite medical treatment, endoscopic therapy with radiofrequency ablation or argon plasma coagulation represents the first option, with appreciable but still suboptimal endoscopic and clinical long-term results [1] [2].
Endoscopic ultrasound-guided gastroenterostomy using a novel dumbbell-shaped fully covered metal stent for afferent loop syndrome with long interluminal distance
Authors: Hideyuki Shiomi, Ryota Nakano, Shogo Ota, Hiroko Iijima
Journal: Endoscopy (2023)

Endoscopic ultrasound-guided gastroenterostomy (EUS-GE) with a lumen-apposing metal stent (LAMS) (Hot Axios; Boston Scientific, USA) effectively manages afferent loop syndrome [1] [2]. The LAMS prevents stent migration and fluid leakage. However, because the distance between the flanges of the LAMS is 10 mm, if the distance between the afferent limb and the stomach increases beyond this distance, the risk of technical failure and complications increases [3].
Bilateral stent-in-stent placement of biliary metal stents with a slim delivery system through an ultraslim endoscope
Authors: Koichiro Mandai, Tomoya Ogawa, Takaaki Yoshimoto
Journal: Endoscopy (2023)

A novel laser-cut-type uncovered self-expandable metal stent (UCSEMS) has recently become available in Japan (Yabusame; Kaneka Medical, Osaka, Japan) [1]. The stent delivery system was 5.4 Fr, with an extremely tapered tip ([Fig. 1]). Here, we describe bilateral stent-in-stent placement of the UCSEMS using an ultraslim endoscope for malignant hilar biliary obstruction with duodenal stenosis.